Abstract Detail

Ancient and ongoing evolutionary leaps in a large gene family with roles in development and defense.

Phylogenies describe the history of gene families and provide critical groundwork for functional studies. Evolutionarily conserved genes are relatively easy to discover and place in a phylogenetic framework, but relationships between genes with structural variation are often harder to resolve. This challenge is amplified in large gene families because of decreased statistical support for deep nodes and internal conflicts in data. The Leucine-Rich Repeat Receptor-like Kinases (LRR-RLKs) are one of the largest plant gene families, and have diverse roles in development and defense. However, the full extent of the LRR-RLK gene family and the relationships between sub-families remain ambiguous. To address this gap in knowledge, we developed a new approach to identify all the members and variants of LRR-RLKs in nine land plant genomes. We discovered that the size of this family and the rate of structural variation has been consistently underestimated. Previously undescribed structural variants such as truncations, conversions, domains gains, and small duplicated fragments are common. The bryophytes have lower LRR-RLK copy number and fewer structural variants than the angiosperms, especially in comparison to the grasses. We also find some genes, previously classified in distantly related families, in our LRR-RLK tree with strong statistical support. The prior misclassification is due to the genes’ superficial resemblance to other families, but our phylogenetic analysis supports the idea that they are truncated LRR-RLKs. These findings highlight the importance of gene structural modification in the evolution of new genes, as well as the utility of this new method for identifying members of large, complex gene families.